The invention discloses a gene chip for detecting six viruses of zoonosis-borne diseases and the application thereof. The gene chip for the viruses of the zoonosis-borne diseases is a gene chip for detecting at least one virus in six viruses of hepatitis E virus, Nipah virus, rabies virus, Rift Valley fever virus, foot and mouth disease virus and Vesicular stomatitis virus, and is fixed with a hepatitis E virus detection probe, a Nipah virus detection probe, a rabies virus detection probe, a Rift Valley fever virus detection probe, a foot and mouth disease virus detection probe and a Vesicular stomatitis virusdetection probe. The invention also discloses a method for detecting the Rift Valley fever virus, the Nipah virus, the foot and mouth disease virus, the Vesicular stomatitis virus, the hepatitis E virus and / or the rabies virus. The invention can stably and specifically implement generic detection of the six viruses of the zoonosis-borne diseases, has the advantages of simpleness, convenience, quickness, good specificity and high sensitivity, and can be used for detecting clinical samples.